The formation of antioxidants and contaminants such as acrylamide (ACR), hydroxymethylfurfural (HMF) and furfural (FUR) during rye bread making was investigated. Flours with extraction rates of 700, 850, 950 and 1 000 g•kg-1 were used. Flour, dough, slice of bread, crust and crumb were analysed. Results are expressed on dry matter basis. Antioxidant capacity of water- and lipid-soluble antioxidants were measured by photochemiluminescence assay. Quencher approach was adapted to total antioxidant capacity and total reducing capacity (Folin-Ciocalteau) methods. Bread based on wholemeal flour showed the highest antioxidant capacity and the lowest levels of potentially harmful compounds (ACR: 50 µg•kg-1; HMF: 33.6 mg•kg-1; FUR: 1.6 mg•kg-1). Estimation of dietary intake of ACR, HMF and FUR from rye bread was 4.93 ng•kg-1•per day, 4.47 µg•kg-1•per day and 0.18 µg•kg-1•per day, respectively. Levels of ACR, HMF and FUR were 27-fold, 631-fold and 31-fold in crust, respetively, which represents less than 15% of the total weight of the bread, compared to crumb. Crust was also the principal contributor to maintain the overall water-soluble antioxidant capacity being up to 3.5-fold more active than crumb or dough. Any mitigation strategy might consider risk and benefits associated with crust.